Predicting the Dynamics and Heterogeneity of Genomic DNA Content within Bacterial Populations across Variable Growth Regimes.

For many applications in microbial synthetic biology, optimizing a desired function requires careful tuning of the degree to which various genes are expressed. One challenge for predicting such effects or interpreting typical characterization experiments is that in bacteria such as E. coli, genome copy number varies widely across different phases and rates of growth, which also impacts how and when genes are expressed from different loci. While such phenomena are relatively well-understood at a mechanistic level, our quantitative understanding of such processes is essentially limited to ideal exponential growth. In contrast, common experimental phenomena such as growth on heterogeneous media, metabolic adaptation, and oxygen restriction all cause substantial deviations from ideal exponential growth, particularly as cultures approach the higher densities at which industrial biomanufacturing and even routine screening experiments are conducted. To meet the need for predicting and explaining how gene dosage impacts cellular functions outside of exponential growth, we here report a novel modeling strategy that leverages agent-based simulation and high performance computing to robustly predict the dynamics and heterogeneity of genomic DNA content within bacterial populations across variable growth regimes. We show that by feeding routine experimental data, such as optical density time series, into our heterogeneous multiphasic growth simulator, we can predict genomic DNA distributions over a range of nonexponential growth conditions. This modeling strategy provides an important advance in the ability of synthetic biologists to evaluate the role of genomic DNA content and heterogeneity in affecting the performance of existing or engineered microbial functions.

Regulation of Bacterial Gene Expression by Protease-Alleviated Spatial Sequestration (PASS).

In natural microbial systems, conditional spatial sequestration of transcription factors enables cells to respond rapidly to changes in their environment or intracellular state by releasing presynthesized regulatory proteins. Although such a mechanism may be useful for engineering synthetic biology technologies ranging from cell-based biosensors to biosynthetic platforms, to date it remains unknown how or whether such conditional spatial sequestration may be engineered. In particular, based upon seemingly contradictory reports in the literature, it is not clear whether subcellular spatial localization of a transcription factor within the cytoplasm is sufficient to preclude regulation of cognate promoters on plasmid-borne or chromosomal loci. Here, we describe a modular, orthogonal platform for investigating and implementing this mechanism using protease-alleviated spatial sequestration (PASS). In this system, expression of an exogenous protease mediates the proteolytic release of engineered transcriptional regulators from the inner face of the Escherichia coli cytoplasmic membrane. We demonstrate that PASS mediates robust, conditional regulation of either transcriptional repression, via tetR, or transcriptional activation, by the λ phage CI protein. This work provides new insights into a biologically important facet of microbial gene expression and establishes a new strategy for engineering conditional transcriptional regulation for the microbial synthetic biology toolbox.

The Hedgehog transcription factor Gli3 modulates angiogenesis.

RATIONALE: The Gli transcription factors are mediators of Hedgehog (Hh) signaling and have been shown to play critical roles during embryogenesis. Previously, we have demonstrated that the Hh pathway is reactivated by ischemia in adult mammals, and that this pathway can be stimulated for therapeutic benefit; however, the specific roles of the Gli transcription factors during ischemia-induced Hh signaling have not been elucidated. OBJECTIVE: To investigate the role of Gli3 in ischemic tissue repair. METHODS AND RESULTS: Gli3-haploinsufficient (Gli3(+/-)) mice and their wild-type littermates were physiologically similar in the absence of ischemia; however, histological assessments of capillary density and echocardiographic measurements of left ventricular ejection fractions were reduced in Gli3(+/-) mice compared to wild-type mice after surgically induced myocardial infarction, and fibrosis was increased. Gli3-deficient mice also displayed reduced capillary density after induction of hindlimb ischemia and an impaired angiogenic response to vascular endothelial growth factor in the corneal angiogenesis model. In endothelial cells, adenovirus-mediated overexpression of Gli3 promoted migration (modified Boyden chamber), small interfering RNA-mediated downregulation of Gli3 delayed tube formation (Matrigel), and Western analyses identified increases in Akt phosphorylation, extracellular signal-regulated kinase (ERK)1/2 activation, and c-Fos expression; however, promoter-reporter assays indicated that Gli3 overexpression does not modulate Gli-dependent transcription. Furthermore, the induction of endothelial cell migration by Gli3 was dependent on Akt and ERK1/2 activation. CONCLUSIONS: Collectively, these observations indicate that Gli3 contributes to vessel growth under both ischemic and nonischemic conditions and provide the first evidence that Gli3 regulates angiogenesis and endothelial cell activity in adult mammals.